PhyCysID: Plant Cystatin Protein Prediction by an Artificial Intelligence Approach

Phytocystatins are proteinaceous inhibitors found in plants that
competitively target various classes of cysteine proteinases, including
papain-like enzymes, cathepsins, and legumains. Based on structural
characteristics and gene organization, phytocystatins can be classified
into four subtypes: intronless (I1 and I2), intron-containing (IwI),
and multidomain cystatins containing more than one inhibitory region
(II). This work presents PhyCysID, a dedicated web server designed
for the rapid classification of phytocystatin subtypes. PhyCysID uses
a set of 21 features derived from amino acid composition, in combination
with 15 distinct machine learning algorithms, to classify phytocystatin
sequences into one of the four subtypes. Initially, the input sequence
is analyzed to verify if it comprises a true phytocystatin sequence.
If so, the input sequence is further analyzed using a specialized
classification pipeline called PhyCysID 12M, which integrates 12 machine
learning models to assign it to one of the four defined phytocystatin
classes. As a case study, a curated dataset of phytocystatin sequences
from the UniProt database was used to evaluate the algorithm’s
performance. The PhyCysID web server enables rapid classification
of both individual and batch-submitted sequences in less than 15 s,
providing high-throughput analysis for an accurate identification
of phytocystatin class and function. PhyCysID is freely available
at https://www.ufrgs.br/labec/phycysid.